[English] 日本語
Yorodumi
- PDB-4bgc: T1 domain of the renal potassium channel Kv1.3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bgc
TitleT1 domain of the renal potassium channel Kv1.3
ComponentsPOTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 3
KeywordsTRANSPORT PROTEIN / ION CHANNEL
Function / homology
Function and homology information


corpus callosum development / voltage-gated monoatomic ion channel activity / Voltage gated Potassium channels / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / optic nerve development / calyx of Held / potassium ion transmembrane transport / voltage-gated potassium channel complex / potassium ion transport ...corpus callosum development / voltage-gated monoatomic ion channel activity / Voltage gated Potassium channels / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / optic nerve development / calyx of Held / potassium ion transmembrane transport / voltage-gated potassium channel complex / potassium ion transport / protein homooligomerization / presynaptic membrane / postsynaptic membrane / membrane raft / axon / glutamatergic synapse / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv1.3 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily ...Potassium channel, voltage dependent, Kv1.3 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily A member 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWeyand, M. / Kremer, W. / Kalbitzer, H.R.
CitationJournal: Protein J. / Year: 2013
Title: 1.2 A X-Ray Structure of the Renal Potassium Channel Kv1.3 T1 Domain.
Authors: Kremer, W. / Weyand, M. / Winklmeier, A. / Schreier, C. / Kalbitzer, H.R.
History
DepositionMar 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 3


Theoretical massNumber of molelcules
Total (without water)12,4181
Polymers12,4181
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.740, 59.740, 62.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

21A-2039-

HOH

-
Components

#1: Protein POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 3 / HGK5 / HLK3 / HPCN3 / VOLTAGE-GATED K(+) CHANNEL HUKIII / VOLTAGE-GATED POTASSIUM CHANNEL SUBUNIT KV1.3


Mass: 12418.116 Da / Num. of mol.: 1 / Fragment: T1 DOMAIN, RESIDUES 104-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: GERMAN RESOURCE CENTER FOR GENOME RESEARCH (RZPD)
Plasmid: PLYSSRARE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P22001
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.7 % / Description: NONE
Crystal growpH: 6.5
Details: WE WANTED TO USE THE PROTEIN IN 150 MM POTASSIUM PHOSPHATE BUFFER PH 6.5 IN 5 MM NMR TUBES FOR CHARACTERIZATION USING NMR SPECTROSCOPY. DURING TESTING, WE OBSERVED THE FORMATION OF CRYSTALS ...Details: WE WANTED TO USE THE PROTEIN IN 150 MM POTASSIUM PHOSPHATE BUFFER PH 6.5 IN 5 MM NMR TUBES FOR CHARACTERIZATION USING NMR SPECTROSCOPY. DURING TESTING, WE OBSERVED THE FORMATION OF CRYSTALS IN THE NMR TUBES. AN INITIAL TEST OF THE CRYSTALS SHOWED AN EXCELLENT DIFFRACTION PATTERN, SO WE DECIDED TO CONTINUE WITH CRYSTALLIZATION OPTIMIZATION IN NMR TUBES, RESULTING IN VERY GOOD CRYSTALS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.950068
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 18, 2005 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.950068 Å / Relative weight: 1
ReflectionResolution: 1.2→45 Å / Num. obs: 33942 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8.6 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QDW

1qdw


Resolution: 1.2→18.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.479 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20463 1537 5 %RANDOM
Rwork0.16297 ---
obs0.16499 29377 90.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.573 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.2→18.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 0 144 1003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.022952
X-RAY DIFFRACTIONr_bond_other_d0.0020.02713
X-RAY DIFFRACTIONr_angle_refined_deg2.2051.9751297
X-RAY DIFFRACTIONr_angle_other_deg1.183.0011694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9495120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19921.40457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77415168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.821516
X-RAY DIFFRACTIONr_chiral_restr0.1550.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
X-RAY DIFFRACTIONr_nbd_refined0.2520.2209
X-RAY DIFFRACTIONr_nbd_other0.220.2784
X-RAY DIFFRACTIONr_nbtor_refined0.1990.2475
X-RAY DIFFRACTIONr_nbtor_other0.1070.2525
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3660.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3640.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8731.5557
X-RAY DIFFRACTIONr_mcbond_other1.2811.5213
X-RAY DIFFRACTIONr_mcangle_it3.6322885
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8593447
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1544.5402
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.56631888
X-RAY DIFFRACTIONr_sphericity_free13.4543144
X-RAY DIFFRACTIONr_sphericity_bonded5.72631633
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 94 -
Rwork0.225 1776 -
obs--75.34 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more